Introduction

Whole genome sequencing (WGS) of parent-offspring trios is a powerful approach for identifying disease-associated genes via detecting copy number variations (CNVs). Existing approaches, which detect CNVs for each individual in a trio independently, usually yield low-detection accuracy. Joint modeling approaches leveraging Mendelian transmission within the parent-offspring trio can be an efficient strategy to improve CNV detection accuracy.In this study, we developed TrioCNV, a novel approach for jointly detecting CNVs in parent-offspring trios from WGS data. Using negative binomial regression, we modeled the read depth signal while considering both GC content bias and mappability bias. Moreover, we incorporated the family relationship and used a hidden Markov model to jointly infer CNVs for three samples of a parent-offspring trio. Through application to both simulated data and a trio from 1000 Genomes Project, we showed that TrioCNV achieved superior performance than existing approaches.The software TrioCNV implemented using a combination of Java and R is freely available from the website at https://github.com/yongzhuang/TrioCNV CONTACT: ydwang@hit.edu.cnSupplementary data are available at Bioinformatics online.

Publications

  1. Joint detection of copy number variations in parent-offspring trios.
    Cite this
    Liu Y, Liu J, Lu J, Peng J, Juan L, Zhu X, Li B, Wang Y, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Yongzhuang Liu
    Developer

    School of Computer Science and Technology, Harbin Institute of Technology, China

  2. Jian Liu
    Developer

    School of Computer Science and Technology, Harbin Institute of Technology, China

  3. Jianguo Lu
    Developer

    School of Computer Science and Technology, Harbin Institute of Technology, China

  4. Jiajie Peng
    Developer

    School of Computer Science and Technology, Harbin Institute of Technology, China

  5. Liran Juan
    Developer

    School of Computer Science and Technology, Harbin Institute of Technology, China

  6. Xiaolin Zhu
    Developer

    Institute for Genomic Medicine, Columbia University

  7. Bingshan Li
    Developer

    Department of Molecular Physiology and Biophysics, Vanderbilt University, United States of America

  8. Yadong Wang
    Investigator

    School of Computer Science and Technology, Harbin Institute of Technology, China

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Summary
AccessionBT001113
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByYadong Wang